Biology subjects

Blanchard, Y.

Publications and source records attributed to Blanchard, Y..

6 recordsLinked to original sources

bioRxiv2026

Epidemic Risks associated with high-temperature replicating infectious hematopoietic necrosis virus (IHNV) field isolates: from molecular characterization to host pathogen interactions

Infectious hematopoietic necrosis virus (IHNV) is a WOAH-notifiable pathogen responsible for severe acute disease in salmonids at temperatures ranging from 4 to 14{degrees}. At higher water temperatures, the disease is generally associated with reduced mortality and lower viral replication. In the context of climate change, rising water temperatures could favor the emergence of thermotolerant strains while representing a major physiological and metabolic stress potentially altering fish's immune responses. This study aims to characterize the impact of increasing water temperatures on IHNV replication and host-pathogen interactions. Following pre-screening, the replication kinetics of the reference strain N61 and two field isolates RtNag0a and SA-22 were characterized in EPC (Epithelioma Papulosum Cyprini) and RTG-2 (Rainbow trout gonad) cell lines at 14, 20 and 22{degrees}. Virulence and host-pathogen interactions were subsequently investigated in vivo in zebrafish (Zf) larvae using complementary microinjection and bath immersion infection models at 21.5 and 23.5{degrees}. In vitro studies revealed distinct thermal replication profiles, distinguishing thermosensitive from thermotolerant isolates, although these phenotypes were influenced by the cellular environment. The zebrafish model enabled the characterization of virulence and antiviral host responses associated with thermotolerant IHNV isolates. Notably, waterborne infection proved effective, contrasting with previous reports describing this exposure route as unsuitable for IHNV studies. These findings expand the growing list of emerging European IHNV genotypes capable of replicating at elevated temperatures (>20{degrees}) and establish zebrafish larvae as a relevant model for virulence assessment of field isolates. Together, these results provide valuable insights into the potential impact of climate warming on IHNV epidemiology and support efforts to predict and anticipate future outbreaks under changing environmental conditions.

pathology↗

bioRxiv2026

Molecular characterization of thermo-adapted Novirhabdovirus variants and virulence in vivo in rainbow trout and zebrafish at different temperatures.

Controlling viral diseases in fish is a challenge for the sustainable development of aquaculture and improving the health of fish farms. Infectious hematopoietic necrosis virus (IHNV) is a major pathogen in aquaculture. It infects cold-water fish, but loses its infectivity at temperatures above 20{degrees}C. Since fish are poikilothermic animals, their body temperature fluctuates according to that of their environment. Faced with current climate change, it is crucial to understand how these pathogens will adapt to rising temperatures. Through a strategy simulating the impact of global warming, this virus has been progressively thermo-adapted to 25{degrees}C. The selected variant, IHNV25, replicates at 25{degrees}C while maintaining efficient replication at low temperatures, like its parental strain. Genome sequencing and a reverse genetics approach revealed that only 9 amino acid substitutions, distributed across 4 of the 6 viral genes, were essential for thermo-adaptation. Although IHNV25 was highly attenuated in its natural host, the rainbow trout, at any temperatures, it proved highly virulent when injected in zebrafish larvae at 20{degrees}C and 25{degrees}C, inducing severe symptoms identical to those observed in trout (hemorrhages, oedema, and exophthalmia). At both temperatures, mortality was preceded by a massive viral replication and a delayed and inefficient interferon and inflammatory response. Unlike the parental strain, IHNV25 was also capable of infecting larvae by bath immersion at 25{degrees}C, entering via the caudal fin, thus demonstrating its ability to cross the species barrier. The identification of viral markers of thermo-adaptation will therefore be of great interest for the epidemiological surveillance of field isolates.

microbiology↗

bioRxiv2024

Major change in swine influenza virus diversity in France owing to emergence and widespread dissemination of a newly introduced H1N2 1C genotype in 2020

Swine influenza A viruses (swIAV) are a major cause of respiratory disease in pigs worldwide, presenting significant economic and health risks. These viruses can reassort, creating new strains with varying pathogenicity and cross-species transmissibility. This study aimed to monitor the genetic and antigenic evolution of swIAV in France from 2019 to 2022. Molecular subtyping revealed a marked increase in H1avN2 cases from 2020 onwards, altering the previously stable subtypes distribution. Whole-genome sequencing and phylogenetic analyses of H1av (1C) strains identified ten circulating genotypes, including five new genotypes, marked by a significant predominance of the H1avN2#E genotype. It was characterized by an HA-1C.2.4, an N2-Gent/84, and internal protein-encoding genes belonging to a newly defined genogroup within the Eurasian avian-like (EA) lineage, the EA-DK subclade. H1avN2#E emerged in Brittany, the countrys most pig-dense region, and rapidly became the most frequently detected swIAV genotype across France. This drastic change in the swIAV lineages proportions at a national scale was unprecedented, making H1avN2#E a unique case for understanding swIAV evolution and spreading patterns. Phylogenetic analyses suggested an introduction of the H1avN2#E genotype from a restricted source, likely originating from Denmark. It spread rapidly with low genetic diversity at the start of the epizootic in 2020, showing increasing diversification in 2021 and 2022, and exhibiting reassortments with other enzootic genotypes. Amino acid sequence alignments of H1avN2#E antigenic sites revealed major mutations and deletions compared to vaccine 1C strain (HA-1C.2.2) and previously predominant H1avN1 strains (HA-1C.2.1). Antigenic cartography confirmed significant antigenic distances between H1avN2#E and other 1C strains, suggesting the new genotype escaped from the swine population preexisting immunity. Epidemiologically, the H1avN2#E virus exhibited epizootic hallmarks with more severe clinical outcomes compared to H1avN1 viruses. These factors likely contributed to the spread of H1avN2#E within the pig population. The rapid rise of H1avN2#E highlighted the dynamic nature of swIAV genetic and antigenic diversity, underscoring the importance of adapted surveillance programs to support risk assessment in the event of new outbreaks. This also demonstrate the need to strengthen biosecurity measures when receiving pigs in a herd and to limit trading of swIAV-excreting live swine between European countries.

evolutionary biology↗

bioRxiv2023

Comparative genomics reveals the emergence of an outbreak-associated Cryptosporidium parvum population in Europe and its spread to the USA

The zoonotic parasite Cryptosporidium parvum is a global cause of gastrointestinal disease in humans and ruminants. Sequence analysis of the highly polymorphic gp60 gene enabled the classification of C. parvum isolates into multiple groups (e.g. IIa, IIc, Id) and a large number of subtypes. In Europe, subtype IIaA15G2R1 is largely predominant and has been associated with many water-and food-borne outbreaks. In this study, we generated new whole genome sequence (WGS) data from 123 human-and ruminant-derived isolates collected in 13 European countries and included other available WGS data from Europe, Egypt, China and the USA (n=72) in the largest comparative genomics study to date. We applied rigorous filters to exclude mixed infections and analysed a dataset from 141 isolates from the zoonotic groups IIa (n=119) and IId (n=22). Based on 28,047 high quality, biallelic genomic SNPs, we identified three distinct and strongly supported populations: isolates from China (IId) and Egypt (IIa and IId) formed population 1, a minority of European isolates (IIa and IId) formed population 2, while the majority of European (IIa, including all IIaA15G2R1 isolates) and all isolates from the USA (IIa) clustered in population 3. Based on analyses of the population structure, population genetics and recombination, we show that population 3 has recently emerged and expanded throughout Europe to then, possibly from the UK, reach the USA where it also expanded. In addition, genetic exchanges between different populations led to the formation of mosaic genomes. The reason(s) for the successful spread of population 3 remained elusive, although genes under selective pressure uniquely in this population were identified.

genomics↗

bioRxiv2023

Investigations on SARS-CoV-2 and other coronaviruses in mink farms in France at the end of the first year of COVID-19 pandemic

Soon after the beginning of the COVID-19 pandemic in early 2020, the Betacoronavirus SARS-CoV-2 infection of several mink farms breeding American minks (Neovison vison) for fur was detected in several countries of Europe. The risk of a new reservoir formation and of a reverse zoonosis from minks was then a major concern. The aim of this study was to investigate the four French mink farms for the circulation of SARS-CoV-2 at the end of 2020. The investigations took place during the slaughtering period thus facilitating different types of sampling (swabs and blood). In one of the four mink farms, 96.6% of serum samples were positive in SARS-CoV-2 ELISA coated with purified N protein recombinant antigen and 54 out of 162 (33%) pharyngo-tracheal swabs were positive by RT-qPCR. The genetic variability among 12 SARS-CoV-2 genomes sequenced in this farm indicated the co-circulation of several lineages at the time of sampling. All SARS-CoV-2 genomes detected were nested within the 20A clade (Nextclade), together with SARS-CoV-2 genomes from humans sampled at the same period. The percentage of SARS-CoV-2 seropositivity by ELISA varied between 0.5 and 1.2% in the three other farms. Interestingly, among these three farms, 11 pharyngo-tracheal swabs and 3 fecal pools from two farms were positive by end-point RT-PCR for an Alphacoronavirus highly similar to a mink coronavirus sequence observed in Danish farms in 2015. In addition, a mink Caliciviridae was identified in one of the two positive farms for Alphacoronavirus. The clinical impact of these unapparent viral infections is not known. The co-infection of SARS-CoV-2 with other viruses in mink farms could contribute to explain the diversity of clinical symptoms noted in different infected farms in Europe. In addition, the co-circulation of an Alphacoronavirus and SARS-CoV-2 within a mink farm would increase potentially the risk of viral recombination between alpha and betacoronaviruses already suggested in wild and domestic animals, as well as in humans. Author summaryFrance is not a country of major mink fur production. Following the SARS-CoV-2 contamination of mink farms in Denmark and the Netherlands, the question arose for the four French farms. The investigation conducted at the same time in the four farms revealed the contamination of one of them by a variant different from the one circulating at the same time in Denmark and the Netherlands mink farms. Investigation of three other farms free of SARS-CoV-2 contamination revealed the circulation of other viruses including a mink Alphacoronavirus and Caliciviridae, which could modify the symptomatology of SARS-CoV-2 infection in minks.

microbiology↗

bioRxiv2021

A world of viruses nested within parasites: Unraveling viral diversity within parasitic flatworms (Platyhelminthes)

Because parasites have an inextricable relationship with their host, they have the potential to serve as viral reservoirs or facilitate virus host-shifts. Yet, little is known about viruses infecting parasitic hosts except for blood-feeding arthropods that are well-known vectors of zoonotic viruses. Herein we uncover viruses of flatworms (Phylum Platyhelminthes, group Neodermata) that specialize in parasitizing vertebrates and their ancestral free-living relatives. We discovered 115 novel viral sequences, including 1 in Macrostomorpha, 5 in Polycladida, 44 in Tricladida, 1 in Monogenea, 15 in Cestoda and 49 in Trematoda, through data mining. The majority of newly identified viruses constitute novel families or genera. Phylogenetic analyses show that the virome of flatworms changed dramatically during the transition of Neodermatans to a parasitic lifestyle. Most Neodermatan viruses seem to co-diversify with their host, with the exception of rhabdoviruses which may switch host more often, based on phylogenetic relationships. Neodermatan rhabodviruses also have an ancestral position to vertebrate-associated viruses, including Lyssaviruses, suggesting that vertebrate rhabdoviruses emerged from a flatworm rhabdovirus in a parasitized host. This study reveals an extensive diversity of viruses in Platyhelminthes and highlights the need to evaluate the role of viral infection in flatworm-associated diseases.

microbiology↗